Starting phenix.real_space_refine on Mon Aug 25 16:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaz_43107/08_2025/8vaz_43107.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 192 5.16 5 C 19068 2.51 5 N 4820 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29404 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "B" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "C" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "D" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "E" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "G" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.25 Number of scatterers: 29404 At special positions: 0 Unit cell: (160.92, 160.92, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 192 16.00 O 5320 8.00 N 4820 7.00 C 19068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 24 sheets defined 56.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.848A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 170 removed outlier: 3.800A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 260 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.597A pdb=" N ASN A 465 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 466 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 472 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.057A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 699 through 704 removed outlier: 4.135A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.817A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 767 removed outlier: 3.556A pdb=" N LEU A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.005A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.617A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 4.016A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.104A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 973 removed outlier: 3.909A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.577A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.804A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 170 removed outlier: 3.792A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.500A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.595A pdb=" N ASN B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 466 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 467 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 472 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.058A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.816A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 767 removed outlier: 3.553A pdb=" N LEU B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.008A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.620A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 917 through 930 removed outlier: 4.017A pdb=" N ASP B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.122A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.909A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1007 removed outlier: 3.575A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.819A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 170 removed outlier: 3.787A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 260 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.593A pdb=" N ASN C 465 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 466 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA C 467 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 472 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.065A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.816A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 767 removed outlier: 3.552A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.010A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 892 removed outlier: 3.624A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 892 " --> pdb=" O GLN C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 917 through 930 removed outlier: 4.014A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.122A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 973 removed outlier: 3.908A pdb=" N ASP C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.579A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.826A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 170 removed outlier: 3.787A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 260 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.596A pdb=" N ASN D 465 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 466 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 467 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 472 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.062A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.819A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 767 removed outlier: 3.551A pdb=" N LEU D 763 " --> pdb=" O SER D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.004A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.622A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 917 through 930 removed outlier: 4.014A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.123A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 973 removed outlier: 3.907A pdb=" N ASP D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1007 removed outlier: 3.579A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 293 removed outlier: 5.040A pdb=" N GLY E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) Proline residue: E 270 - end of helix Processing helix chain 'F' and resid 259 through 293 removed outlier: 4.869A pdb=" N GLY F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 259 through 293 removed outlier: 5.008A pdb=" N GLY G 269 " --> pdb=" O VAL G 265 " (cutoff:3.500A) Proline residue: G 270 - end of helix Processing helix chain 'H' and resid 259 through 293 removed outlier: 4.616A pdb=" N GLY H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 401 removed outlier: 8.671A pdb=" N GLU A 399 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR A 401 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.319A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.446A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 4.231A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 401 removed outlier: 8.749A pdb=" N GLU B 399 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR B 401 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 377 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.869A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.317A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.448A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 975 through 981 removed outlier: 4.191A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 401 removed outlier: 8.751A pdb=" N GLU C 399 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR C 401 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.319A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.445A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 975 through 981 removed outlier: 4.221A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 401 removed outlier: 8.660A pdb=" N GLU D 399 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 375 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR D 401 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE D 377 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.327A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.446A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 975 through 981 removed outlier: 4.190A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1476 hydrogen bonds defined for protein. 4074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9286 1.34 - 1.46: 6479 1.46 - 1.58: 14019 1.58 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 30068 Sorted by residual: bond pdb=" C PRO A 191 " pdb=" N PRO A 192 " ideal model delta sigma weight residual 1.335 1.350 -0.014 1.36e-02 5.41e+03 1.09e+00 bond pdb=" CA VAL D 190 " pdb=" C VAL D 190 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.05e-02 9.07e+03 1.06e+00 bond pdb=" C PRO C 191 " pdb=" N PRO C 192 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 9.97e-01 bond pdb=" C PRO B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.77e-01 bond pdb=" C PRO D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.36e-02 5.41e+03 9.08e-01 ... (remaining 30063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39996 1.43 - 2.85: 648 2.85 - 4.28: 110 4.28 - 5.71: 46 5.71 - 7.13: 12 Bond angle restraints: 40812 Sorted by residual: angle pdb=" C TYR C1015 " pdb=" CA TYR C1015 " pdb=" CB TYR C1015 " ideal model delta sigma weight residual 110.62 114.17 -3.55 1.51e+00 4.39e-01 5.53e+00 angle pdb=" C TYR D1015 " pdb=" CA TYR D1015 " pdb=" CB TYR D1015 " ideal model delta sigma weight residual 110.62 114.12 -3.50 1.51e+00 4.39e-01 5.37e+00 angle pdb=" CA ARG C 167 " pdb=" CB ARG C 167 " pdb=" CG ARG C 167 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA ARG B 167 " pdb=" CB ARG B 167 " pdb=" CG ARG B 167 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 angle pdb=" CA ARG D 167 " pdb=" CB ARG D 167 " pdb=" CG ARG D 167 " ideal model delta sigma weight residual 114.10 118.48 -4.38 2.00e+00 2.50e-01 4.79e+00 ... (remaining 40807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 16849 17.65 - 35.30: 756 35.30 - 52.95: 99 52.95 - 70.60: 12 70.60 - 88.25: 8 Dihedral angle restraints: 17724 sinusoidal: 6892 harmonic: 10832 Sorted by residual: dihedral pdb=" CA TYR C1015 " pdb=" C TYR C1015 " pdb=" N ARG C1016 " pdb=" CA ARG C1016 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR D1015 " pdb=" C TYR D1015 " pdb=" N ARG D1016 " pdb=" CA ARG D1016 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR B1015 " pdb=" C TYR B1015 " pdb=" N ARG B1016 " pdb=" CA ARG B1016 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3160 0.036 - 0.072: 1150 0.072 - 0.109: 301 0.109 - 0.145: 80 0.145 - 0.181: 9 Chirality restraints: 4700 Sorted by residual: chirality pdb=" CB VAL A 792 " pdb=" CA VAL A 792 " pdb=" CG1 VAL A 792 " pdb=" CG2 VAL A 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB VAL B 792 " pdb=" CA VAL B 792 " pdb=" CG1 VAL B 792 " pdb=" CG2 VAL B 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CB VAL C 792 " pdb=" CA VAL C 792 " pdb=" CG1 VAL C 792 " pdb=" CG2 VAL C 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 4697 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A 192 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1015 " -0.015 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR C1015 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C1015 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C1015 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C1015 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C1015 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C1015 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C1015 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1015 " 0.015 2.00e-02 2.50e+03 1.35e-02 3.63e+00 pdb=" CG TYR D1015 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D1015 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D1015 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D1015 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D1015 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D1015 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D1015 " -0.000 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 9951 2.85 - 3.42: 32083 3.42 - 4.00: 54101 4.00 - 4.57: 77186 4.57 - 5.14: 111931 Nonbonded interactions: 285252 Sorted by model distance: nonbonded pdb=" OG1 THR B 284 " pdb=" OH TYR C 290 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.284 3.040 nonbonded pdb=" O VAL A 185 " pdb=" OG1 THR A 189 " model vdw 2.310 3.040 ... (remaining 285247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30068 Z= 0.115 Angle : 0.502 7.133 40812 Z= 0.263 Chirality : 0.042 0.181 4700 Planarity : 0.004 0.059 5116 Dihedral : 10.165 88.251 10708 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.14), residues: 3664 helix: 0.80 (0.12), residues: 1880 sheet: 0.39 (0.25), residues: 456 loop : 0.22 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.034 0.001 TYR C1015 PHE 0.032 0.002 PHE D 194 TRP 0.023 0.001 TRP D 23 HIS 0.002 0.001 HIS C 718 Details of bonding type rmsd covalent geometry : bond 0.00244 (30068) covalent geometry : angle 0.50170 (40812) hydrogen bonds : bond 0.14953 ( 1476) hydrogen bonds : angle 5.38269 ( 4074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7741 (p90) cc_final: 0.6887 (t60) REVERT: A 372 ASN cc_start: 0.7127 (t0) cc_final: 0.6668 (t0) REVERT: B 23 TRP cc_start: 0.7725 (p90) cc_final: 0.6880 (t60) REVERT: B 157 ASN cc_start: 0.8636 (m110) cc_final: 0.8338 (t0) REVERT: B 159 PHE cc_start: 0.8287 (t80) cc_final: 0.7874 (t80) REVERT: B 198 TYR cc_start: 0.8544 (t80) cc_final: 0.8318 (t80) REVERT: B 372 ASN cc_start: 0.7211 (t0) cc_final: 0.6764 (t0) REVERT: C 372 ASN cc_start: 0.7209 (t0) cc_final: 0.6754 (t0) REVERT: D 23 TRP cc_start: 0.7714 (p90) cc_final: 0.6928 (t60) REVERT: D 159 PHE cc_start: 0.8285 (t80) cc_final: 0.7928 (t80) REVERT: D 372 ASN cc_start: 0.7113 (t0) cc_final: 0.6665 (t0) REVERT: E 260 ARG cc_start: 0.5468 (mtt180) cc_final: 0.4556 (mmt180) REVERT: F 260 ARG cc_start: 0.5927 (mtt180) cc_final: 0.4863 (tpt90) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.7048 time to fit residues: 293.4216 Evaluate side-chains 232 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN B 957 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055975 restraints weight = 73617.255| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.39 r_work: 0.2748 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30068 Z= 0.169 Angle : 0.549 11.878 40812 Z= 0.279 Chirality : 0.042 0.186 4700 Planarity : 0.004 0.038 5116 Dihedral : 3.624 17.881 3964 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.39 % Allowed : 6.55 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3664 helix: 1.20 (0.12), residues: 1852 sheet: 0.50 (0.25), residues: 452 loop : 0.62 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 393 TYR 0.026 0.001 TYR C1015 PHE 0.020 0.001 PHE A 144 TRP 0.014 0.001 TRP D 23 HIS 0.003 0.001 HIS D 718 Details of bonding type rmsd covalent geometry : bond 0.00397 (30068) covalent geometry : angle 0.54897 (40812) hydrogen bonds : bond 0.04680 ( 1476) hydrogen bonds : angle 4.50069 ( 4074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9306 (mmm) cc_final: 0.8847 (ptt) REVERT: A 154 MET cc_start: 0.8289 (tpp) cc_final: 0.7909 (tpt) REVERT: A 372 ASN cc_start: 0.7050 (t0) cc_final: 0.6556 (t0) REVERT: B 30 MET cc_start: 0.9339 (mmm) cc_final: 0.8834 (ptt) REVERT: B 154 MET cc_start: 0.8340 (tpp) cc_final: 0.7964 (tpp) REVERT: B 159 PHE cc_start: 0.8241 (t80) cc_final: 0.7803 (t80) REVERT: B 198 TYR cc_start: 0.8571 (t80) cc_final: 0.8119 (t80) REVERT: B 372 ASN cc_start: 0.7104 (t0) cc_final: 0.6619 (t0) REVERT: B 574 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7855 (p0) REVERT: B 806 ASN cc_start: 0.8638 (t0) cc_final: 0.8419 (m-40) REVERT: C 30 MET cc_start: 0.9357 (mmm) cc_final: 0.8913 (ptm) REVERT: C 154 MET cc_start: 0.8562 (tpp) cc_final: 0.8170 (tpp) REVERT: C 159 PHE cc_start: 0.8502 (t80) cc_final: 0.8235 (t80) REVERT: C 372 ASN cc_start: 0.7177 (t0) cc_final: 0.6690 (t0) REVERT: C 574 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7879 (p0) REVERT: C 806 ASN cc_start: 0.8643 (t0) cc_final: 0.8423 (m-40) REVERT: D 30 MET cc_start: 0.9291 (mmm) cc_final: 0.8777 (ptt) REVERT: D 154 MET cc_start: 0.8518 (tpp) cc_final: 0.8106 (tpp) REVERT: D 159 PHE cc_start: 0.8270 (t80) cc_final: 0.8069 (t80) REVERT: D 198 TYR cc_start: 0.8680 (t80) cc_final: 0.8151 (t80) REVERT: D 372 ASN cc_start: 0.7045 (t0) cc_final: 0.6565 (t0) REVERT: E 260 ARG cc_start: 0.5773 (mtt180) cc_final: 0.4598 (tpt90) REVERT: E 266 TYR cc_start: 0.8489 (m-10) cc_final: 0.8210 (m-80) REVERT: E 268 LEU cc_start: 0.9039 (tt) cc_final: 0.8718 (tt) REVERT: F 260 ARG cc_start: 0.5489 (mtt180) cc_final: 0.4080 (tpt90) REVERT: G 266 TYR cc_start: 0.8136 (m-10) cc_final: 0.7761 (m-80) REVERT: H 259 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6121 (mp) REVERT: H 291 ARG cc_start: 0.7654 (mmp-170) cc_final: 0.6597 (mmp80) outliers start: 45 outliers final: 16 residues processed: 274 average time/residue: 0.5929 time to fit residues: 196.8519 Evaluate side-chains 251 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 334 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054920 restraints weight = 73954.302| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.38 r_work: 0.2720 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 30068 Z= 0.200 Angle : 0.555 13.908 40812 Z= 0.278 Chirality : 0.042 0.153 4700 Planarity : 0.003 0.033 5116 Dihedral : 3.618 16.424 3964 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.67 % Allowed : 7.79 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.14), residues: 3664 helix: 1.13 (0.12), residues: 1880 sheet: 0.50 (0.25), residues: 452 loop : 0.57 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 329 TYR 0.022 0.001 TYR A1015 PHE 0.025 0.001 PHE A 159 TRP 0.011 0.001 TRP D 275 HIS 0.003 0.001 HIS B 718 Details of bonding type rmsd covalent geometry : bond 0.00474 (30068) covalent geometry : angle 0.55496 (40812) hydrogen bonds : bond 0.04633 ( 1476) hydrogen bonds : angle 4.40624 ( 4074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9225 (mmm) cc_final: 0.8759 (ptm) REVERT: A 154 MET cc_start: 0.8726 (tpp) cc_final: 0.8518 (tpp) REVERT: A 372 ASN cc_start: 0.6963 (t0) cc_final: 0.6454 (t0) REVERT: A 739 MET cc_start: 0.9470 (mtm) cc_final: 0.9223 (mtp) REVERT: B 30 MET cc_start: 0.9359 (mmm) cc_final: 0.8823 (ptt) REVERT: B 153 ASP cc_start: 0.8485 (t0) cc_final: 0.8272 (t0) REVERT: B 154 MET cc_start: 0.8576 (tpp) cc_final: 0.8125 (tpp) REVERT: B 198 TYR cc_start: 0.8775 (t80) cc_final: 0.8518 (t80) REVERT: B 372 ASN cc_start: 0.6992 (t0) cc_final: 0.6469 (t0) REVERT: B 574 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7880 (p0) REVERT: B 739 MET cc_start: 0.9467 (mtm) cc_final: 0.9224 (mtp) REVERT: B 806 ASN cc_start: 0.8727 (t0) cc_final: 0.8495 (m-40) REVERT: B 807 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: C 30 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8995 (ptt) REVERT: C 154 MET cc_start: 0.8887 (tpp) cc_final: 0.8604 (tpp) REVERT: C 159 PHE cc_start: 0.8415 (t80) cc_final: 0.8096 (t80) REVERT: C 372 ASN cc_start: 0.6993 (t0) cc_final: 0.6463 (t0) REVERT: C 739 MET cc_start: 0.9471 (mtm) cc_final: 0.9225 (mtp) REVERT: C 806 ASN cc_start: 0.8734 (t0) cc_final: 0.8502 (m-40) REVERT: C 807 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: D 23 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7138 (p-90) REVERT: D 154 MET cc_start: 0.8655 (tpp) cc_final: 0.8372 (tpp) REVERT: D 198 TYR cc_start: 0.8832 (t80) cc_final: 0.8447 (t80) REVERT: D 372 ASN cc_start: 0.6923 (t0) cc_final: 0.6446 (t0) REVERT: D 739 MET cc_start: 0.9473 (mtm) cc_final: 0.9241 (mtp) REVERT: E 260 ARG cc_start: 0.5777 (mtt180) cc_final: 0.4601 (tpt90) REVERT: F 260 ARG cc_start: 0.5446 (mtt180) cc_final: 0.4108 (tpt90) REVERT: F 262 LEU cc_start: 0.8947 (pp) cc_final: 0.8676 (pp) REVERT: F 266 TYR cc_start: 0.8490 (m-80) cc_final: 0.8192 (m-80) REVERT: G 266 TYR cc_start: 0.8241 (m-10) cc_final: 0.7964 (m-80) REVERT: H 291 ARG cc_start: 0.7712 (mmp-170) cc_final: 0.6602 (mmp80) outliers start: 54 outliers final: 18 residues processed: 268 average time/residue: 0.5918 time to fit residues: 192.1982 Evaluate side-chains 258 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 807 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 207 optimal weight: 0.0010 chunk 42 optimal weight: 0.0030 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 0.0270 chunk 108 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057794 restraints weight = 73303.615| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.37 r_work: 0.2784 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30068 Z= 0.095 Angle : 0.483 11.856 40812 Z= 0.241 Chirality : 0.039 0.136 4700 Planarity : 0.003 0.035 5116 Dihedral : 3.446 14.214 3964 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.48 % Allowed : 8.93 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.14), residues: 3664 helix: 1.46 (0.12), residues: 1848 sheet: 0.63 (0.26), residues: 452 loop : 0.76 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 329 TYR 0.019 0.001 TYR H 266 PHE 0.026 0.001 PHE A 159 TRP 0.008 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00198 (30068) covalent geometry : angle 0.48273 (40812) hydrogen bonds : bond 0.03535 ( 1476) hydrogen bonds : angle 4.10393 ( 4074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9357 (mmm) cc_final: 0.8929 (ptm) REVERT: A 154 MET cc_start: 0.8960 (tpp) cc_final: 0.8670 (tpp) REVERT: A 372 ASN cc_start: 0.6752 (t0) cc_final: 0.6275 (t0) REVERT: B 153 ASP cc_start: 0.8470 (t0) cc_final: 0.8247 (t0) REVERT: B 154 MET cc_start: 0.8652 (tpp) cc_final: 0.8334 (tpp) REVERT: B 159 PHE cc_start: 0.8298 (t80) cc_final: 0.8035 (t80) REVERT: B 198 TYR cc_start: 0.8902 (t80) cc_final: 0.8498 (t80) REVERT: B 372 ASN cc_start: 0.6926 (t0) cc_final: 0.6421 (t0) REVERT: B 574 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 806 ASN cc_start: 0.8625 (t0) cc_final: 0.8386 (m-40) REVERT: C 30 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9146 (mmm) REVERT: C 154 MET cc_start: 0.8889 (tpp) cc_final: 0.8304 (tpp) REVERT: C 159 PHE cc_start: 0.8411 (t80) cc_final: 0.8038 (t80) REVERT: C 372 ASN cc_start: 0.6922 (t0) cc_final: 0.6410 (t0) REVERT: C 806 ASN cc_start: 0.8626 (t0) cc_final: 0.8386 (m-40) REVERT: D 154 MET cc_start: 0.8818 (tpp) cc_final: 0.8407 (tpp) REVERT: D 198 TYR cc_start: 0.8822 (t80) cc_final: 0.8435 (t80) REVERT: D 372 ASN cc_start: 0.6739 (t0) cc_final: 0.6266 (t0) REVERT: E 260 ARG cc_start: 0.5351 (mtt180) cc_final: 0.4048 (mtp180) REVERT: E 266 TYR cc_start: 0.8409 (m-80) cc_final: 0.7898 (m-80) REVERT: F 260 ARG cc_start: 0.5251 (mtt180) cc_final: 0.3771 (mtp180) REVERT: F 262 LEU cc_start: 0.9004 (pp) cc_final: 0.8752 (pp) REVERT: G 266 TYR cc_start: 0.8226 (m-10) cc_final: 0.7947 (m-80) REVERT: H 262 LEU cc_start: 0.8638 (pp) cc_final: 0.8362 (pp) REVERT: H 266 TYR cc_start: 0.8146 (m-10) cc_final: 0.7908 (m-80) outliers start: 48 outliers final: 13 residues processed: 266 average time/residue: 0.5575 time to fit residues: 182.5964 Evaluate side-chains 246 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 181 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.084861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055397 restraints weight = 73317.878| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.30 r_work: 0.2727 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 30068 Z= 0.195 Angle : 0.549 9.998 40812 Z= 0.271 Chirality : 0.042 0.153 4700 Planarity : 0.003 0.035 5116 Dihedral : 3.504 14.120 3964 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.93 % Allowed : 9.98 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.14), residues: 3664 helix: 1.26 (0.12), residues: 1888 sheet: 0.63 (0.25), residues: 452 loop : 0.71 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 329 TYR 0.025 0.001 TYR F 266 PHE 0.029 0.001 PHE A 159 TRP 0.010 0.001 TRP B 275 HIS 0.003 0.001 HIS D 718 Details of bonding type rmsd covalent geometry : bond 0.00465 (30068) covalent geometry : angle 0.54876 (40812) hydrogen bonds : bond 0.04285 ( 1476) hydrogen bonds : angle 4.18241 ( 4074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9412 (mmm) cc_final: 0.8943 (ptm) REVERT: A 154 MET cc_start: 0.9013 (tpp) cc_final: 0.8746 (tpp) REVERT: A 372 ASN cc_start: 0.6761 (t0) cc_final: 0.6288 (t0) REVERT: B 30 MET cc_start: 0.9354 (mmm) cc_final: 0.8920 (ptt) REVERT: B 153 ASP cc_start: 0.8490 (t0) cc_final: 0.8250 (t0) REVERT: B 154 MET cc_start: 0.8641 (tpp) cc_final: 0.8363 (tpp) REVERT: B 198 TYR cc_start: 0.8904 (t80) cc_final: 0.8628 (t80) REVERT: B 372 ASN cc_start: 0.6944 (t0) cc_final: 0.6295 (t0) REVERT: B 574 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 806 ASN cc_start: 0.8756 (t0) cc_final: 0.8519 (t0) REVERT: C 154 MET cc_start: 0.8892 (tpp) cc_final: 0.8241 (tpp) REVERT: C 198 TYR cc_start: 0.8808 (t80) cc_final: 0.8402 (t80) REVERT: C 372 ASN cc_start: 0.6934 (t0) cc_final: 0.6280 (t0) REVERT: C 806 ASN cc_start: 0.8765 (t0) cc_final: 0.8529 (t0) REVERT: D 154 MET cc_start: 0.8760 (tpp) cc_final: 0.8321 (tpp) REVERT: D 198 TYR cc_start: 0.8794 (t80) cc_final: 0.8370 (t80) REVERT: D 372 ASN cc_start: 0.6750 (t0) cc_final: 0.6284 (t0) REVERT: E 260 ARG cc_start: 0.5226 (mtt180) cc_final: 0.3751 (mtp180) REVERT: E 266 TYR cc_start: 0.8427 (m-80) cc_final: 0.7918 (m-80) REVERT: F 260 ARG cc_start: 0.5106 (mtt180) cc_final: 0.3728 (mtp180) REVERT: F 262 LEU cc_start: 0.9048 (pp) cc_final: 0.8817 (pp) REVERT: F 266 TYR cc_start: 0.8368 (m-10) cc_final: 0.8091 (m-80) REVERT: G 266 TYR cc_start: 0.8270 (m-10) cc_final: 0.7982 (m-80) REVERT: H 262 LEU cc_start: 0.8645 (pp) cc_final: 0.8321 (pp) outliers start: 30 outliers final: 14 residues processed: 251 average time/residue: 0.5352 time to fit residues: 163.8536 Evaluate side-chains 246 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 314 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 322 optimal weight: 0.0010 chunk 316 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 53 optimal weight: 0.0010 chunk 105 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057572 restraints weight = 72373.270| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.30 r_work: 0.2780 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30068 Z= 0.100 Angle : 0.510 11.293 40812 Z= 0.249 Chirality : 0.039 0.153 4700 Planarity : 0.003 0.038 5116 Dihedral : 3.425 13.514 3964 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.11 % Allowed : 9.95 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.14), residues: 3664 helix: 1.44 (0.12), residues: 1876 sheet: 0.72 (0.25), residues: 452 loop : 0.82 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 329 TYR 0.023 0.001 TYR H 266 PHE 0.031 0.001 PHE D 159 TRP 0.009 0.001 TRP B 275 HIS 0.002 0.000 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00219 (30068) covalent geometry : angle 0.51019 (40812) hydrogen bonds : bond 0.03513 ( 1476) hydrogen bonds : angle 4.02409 ( 4074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9444 (mmm) cc_final: 0.8926 (ptm) REVERT: A 154 MET cc_start: 0.8950 (tpp) cc_final: 0.8729 (tpp) REVERT: A 372 ASN cc_start: 0.6691 (t0) cc_final: 0.6061 (t0) REVERT: B 30 MET cc_start: 0.9355 (mmm) cc_final: 0.8930 (ptt) REVERT: B 153 ASP cc_start: 0.8483 (t0) cc_final: 0.8246 (t0) REVERT: B 154 MET cc_start: 0.8622 (tpp) cc_final: 0.8397 (tpp) REVERT: B 198 TYR cc_start: 0.8991 (t80) cc_final: 0.8499 (t80) REVERT: B 252 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 372 ASN cc_start: 0.6843 (t0) cc_final: 0.6161 (t0) REVERT: B 574 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 806 ASN cc_start: 0.8706 (t0) cc_final: 0.8430 (t0) REVERT: C 30 MET cc_start: 0.9453 (mmm) cc_final: 0.8927 (ptm) REVERT: C 154 MET cc_start: 0.8826 (tpp) cc_final: 0.8308 (tpp) REVERT: C 372 ASN cc_start: 0.6852 (t0) cc_final: 0.6166 (t0) REVERT: C 806 ASN cc_start: 0.8703 (t0) cc_final: 0.8430 (t0) REVERT: D 154 MET cc_start: 0.8760 (tpp) cc_final: 0.8313 (tpp) REVERT: D 198 TYR cc_start: 0.8740 (t80) cc_final: 0.8354 (t80) REVERT: D 252 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8174 (t80) REVERT: D 372 ASN cc_start: 0.6676 (t0) cc_final: 0.6039 (t0) REVERT: E 260 ARG cc_start: 0.5162 (mtt180) cc_final: 0.3724 (mtp180) REVERT: E 266 TYR cc_start: 0.8423 (m-80) cc_final: 0.7939 (m-80) REVERT: F 260 ARG cc_start: 0.5050 (mtt180) cc_final: 0.3700 (mtp180) REVERT: G 266 TYR cc_start: 0.8249 (m-10) cc_final: 0.8010 (m-80) REVERT: H 266 TYR cc_start: 0.7987 (m-10) cc_final: 0.7771 (m-10) outliers start: 36 outliers final: 20 residues processed: 264 average time/residue: 0.4833 time to fit residues: 156.6257 Evaluate side-chains 254 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 257 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 294 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 233 optimal weight: 0.0060 chunk 44 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056191 restraints weight = 73801.189| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.38 r_work: 0.2752 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30068 Z= 0.136 Angle : 0.549 13.651 40812 Z= 0.264 Chirality : 0.041 0.168 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.425 13.656 3964 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.05 % Allowed : 10.60 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.14), residues: 3664 helix: 1.37 (0.12), residues: 1896 sheet: 0.68 (0.25), residues: 452 loop : 0.79 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 329 TYR 0.021 0.001 TYR F 266 PHE 0.030 0.001 PHE A 144 TRP 0.009 0.001 TRP B 275 HIS 0.002 0.001 HIS D 718 Details of bonding type rmsd covalent geometry : bond 0.00319 (30068) covalent geometry : angle 0.54879 (40812) hydrogen bonds : bond 0.03777 ( 1476) hydrogen bonds : angle 4.06194 ( 4074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9409 (mmm) cc_final: 0.8911 (ptm) REVERT: A 252 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 372 ASN cc_start: 0.6728 (t0) cc_final: 0.6090 (t0) REVERT: B 30 MET cc_start: 0.9357 (mmm) cc_final: 0.8968 (ptt) REVERT: B 153 ASP cc_start: 0.8520 (t0) cc_final: 0.8278 (t0) REVERT: B 198 TYR cc_start: 0.9015 (t80) cc_final: 0.8605 (t80) REVERT: B 372 ASN cc_start: 0.6860 (t0) cc_final: 0.6214 (t0) REVERT: B 806 ASN cc_start: 0.8718 (t0) cc_final: 0.8454 (t0) REVERT: C 30 MET cc_start: 0.9391 (mmm) cc_final: 0.8904 (ptm) REVERT: C 154 MET cc_start: 0.8835 (tpp) cc_final: 0.8288 (tpp) REVERT: C 198 TYR cc_start: 0.8815 (t80) cc_final: 0.8431 (t80) REVERT: C 252 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8144 (t80) REVERT: C 372 ASN cc_start: 0.6866 (t0) cc_final: 0.6218 (t0) REVERT: C 806 ASN cc_start: 0.8713 (t0) cc_final: 0.8452 (t0) REVERT: D 154 MET cc_start: 0.8773 (tpp) cc_final: 0.8334 (tpp) REVERT: D 198 TYR cc_start: 0.8761 (t80) cc_final: 0.8399 (t80) REVERT: D 372 ASN cc_start: 0.6702 (t0) cc_final: 0.6056 (t0) REVERT: E 260 ARG cc_start: 0.4993 (mtt180) cc_final: 0.3670 (mtp180) REVERT: E 266 TYR cc_start: 0.8392 (m-80) cc_final: 0.7904 (m-80) REVERT: F 260 ARG cc_start: 0.4195 (mtt180) cc_final: 0.2997 (mtp180) REVERT: F 262 LEU cc_start: 0.8924 (pp) cc_final: 0.8666 (pt) REVERT: F 266 TYR cc_start: 0.8224 (m-10) cc_final: 0.7995 (m-80) REVERT: G 266 TYR cc_start: 0.8245 (m-10) cc_final: 0.7997 (m-80) REVERT: H 262 LEU cc_start: 0.8724 (pp) cc_final: 0.8400 (pt) REVERT: H 266 TYR cc_start: 0.8009 (m-10) cc_final: 0.7740 (m-10) outliers start: 34 outliers final: 19 residues processed: 254 average time/residue: 0.5384 time to fit residues: 167.9927 Evaluate side-chains 249 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 84 optimal weight: 0.9980 chunk 356 optimal weight: 30.0000 chunk 34 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 233 optimal weight: 0.0040 chunk 302 optimal weight: 10.0000 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.087233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058140 restraints weight = 72914.356| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.32 r_work: 0.2782 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30068 Z= 0.105 Angle : 0.554 15.956 40812 Z= 0.263 Chirality : 0.040 0.149 4700 Planarity : 0.003 0.038 5116 Dihedral : 3.383 13.241 3964 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.05 % Allowed : 10.54 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.14), residues: 3664 helix: 1.45 (0.12), residues: 1888 sheet: 0.72 (0.25), residues: 452 loop : 0.83 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.015 0.001 TYR F 266 PHE 0.028 0.001 PHE C 159 TRP 0.009 0.001 TRP D 275 HIS 0.002 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00235 (30068) covalent geometry : angle 0.55358 (40812) hydrogen bonds : bond 0.03447 ( 1476) hydrogen bonds : angle 3.98722 ( 4074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9429 (mmm) cc_final: 0.8896 (ptm) REVERT: A 252 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8132 (t80) REVERT: A 372 ASN cc_start: 0.6690 (t0) cc_final: 0.6044 (t0) REVERT: B 154 MET cc_start: 0.8619 (tpp) cc_final: 0.8025 (tpp) REVERT: B 198 TYR cc_start: 0.8864 (t80) cc_final: 0.8555 (t80) REVERT: B 252 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 372 ASN cc_start: 0.6850 (t0) cc_final: 0.6211 (t0) REVERT: B 712 MET cc_start: 0.9023 (tmm) cc_final: 0.8752 (ppp) REVERT: B 806 ASN cc_start: 0.8702 (t0) cc_final: 0.8442 (t0) REVERT: C 30 MET cc_start: 0.9439 (mmm) cc_final: 0.8964 (ptt) REVERT: C 154 MET cc_start: 0.8832 (tpp) cc_final: 0.8272 (tpp) REVERT: C 198 TYR cc_start: 0.8882 (t80) cc_final: 0.8505 (t80) REVERT: C 252 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8145 (t80) REVERT: C 372 ASN cc_start: 0.6854 (t0) cc_final: 0.6184 (t0) REVERT: C 806 ASN cc_start: 0.8696 (t0) cc_final: 0.8439 (t0) REVERT: D 154 MET cc_start: 0.8815 (tpp) cc_final: 0.8401 (tpp) REVERT: D 198 TYR cc_start: 0.8750 (t80) cc_final: 0.8377 (t80) REVERT: D 252 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (t80) REVERT: D 372 ASN cc_start: 0.6680 (t0) cc_final: 0.6039 (t0) REVERT: D 712 MET cc_start: 0.9021 (tmm) cc_final: 0.8753 (ppp) REVERT: E 260 ARG cc_start: 0.4977 (mtt180) cc_final: 0.3762 (mtp180) REVERT: E 266 TYR cc_start: 0.8344 (m-80) cc_final: 0.7837 (m-80) REVERT: F 260 ARG cc_start: 0.4442 (mtt180) cc_final: 0.2994 (mtp180) REVERT: G 266 TYR cc_start: 0.8216 (m-10) cc_final: 0.7981 (m-80) REVERT: H 262 LEU cc_start: 0.8752 (pp) cc_final: 0.8310 (pt) outliers start: 34 outliers final: 18 residues processed: 255 average time/residue: 0.5322 time to fit residues: 165.4129 Evaluate side-chains 249 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 123 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 chunk 365 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 168 optimal weight: 0.0670 chunk 193 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057750 restraints weight = 72738.070| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.26 r_work: 0.2757 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30068 Z= 0.124 Angle : 0.571 16.079 40812 Z= 0.273 Chirality : 0.040 0.160 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.380 13.493 3964 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.96 % Allowed : 11.00 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.14), residues: 3664 helix: 1.40 (0.12), residues: 1896 sheet: 0.70 (0.25), residues: 452 loop : 0.82 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 329 TYR 0.019 0.001 TYR F 266 PHE 0.029 0.001 PHE B 159 TRP 0.008 0.001 TRP D 275 HIS 0.002 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00289 (30068) covalent geometry : angle 0.57056 (40812) hydrogen bonds : bond 0.03611 ( 1476) hydrogen bonds : angle 4.01383 ( 4074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9435 (mmm) cc_final: 0.8789 (ptt) REVERT: A 154 MET cc_start: 0.9142 (tpt) cc_final: 0.8796 (tpp) REVERT: A 198 TYR cc_start: 0.8891 (t80) cc_final: 0.8571 (t80) REVERT: A 252 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8142 (t80) REVERT: A 372 ASN cc_start: 0.6732 (t0) cc_final: 0.6007 (t0) REVERT: B 154 MET cc_start: 0.8619 (tpp) cc_final: 0.8124 (tpp) REVERT: B 198 TYR cc_start: 0.8947 (t80) cc_final: 0.8520 (t80) REVERT: B 252 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 372 ASN cc_start: 0.6858 (t0) cc_final: 0.6220 (t0) REVERT: B 806 ASN cc_start: 0.8675 (t0) cc_final: 0.8401 (t0) REVERT: C 30 MET cc_start: 0.9418 (mmm) cc_final: 0.8944 (ptt) REVERT: C 154 MET cc_start: 0.8861 (tpp) cc_final: 0.8323 (tpp) REVERT: C 198 TYR cc_start: 0.8888 (t80) cc_final: 0.8523 (t80) REVERT: C 252 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (t80) REVERT: C 806 ASN cc_start: 0.8671 (t0) cc_final: 0.8399 (t0) REVERT: D 154 MET cc_start: 0.8784 (tpp) cc_final: 0.8450 (tpp) REVERT: D 198 TYR cc_start: 0.8793 (t80) cc_final: 0.8385 (t80) REVERT: D 252 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8186 (t80) REVERT: D 372 ASN cc_start: 0.6716 (t0) cc_final: 0.5992 (t0) REVERT: E 260 ARG cc_start: 0.5428 (mtt180) cc_final: 0.4022 (mmt180) REVERT: E 266 TYR cc_start: 0.8371 (m-80) cc_final: 0.7869 (m-80) REVERT: F 260 ARG cc_start: 0.4424 (mtt180) cc_final: 0.2955 (mtp180) REVERT: G 266 TYR cc_start: 0.8215 (m-10) cc_final: 0.7977 (m-80) outliers start: 31 outliers final: 22 residues processed: 246 average time/residue: 0.5172 time to fit residues: 155.0501 Evaluate side-chains 253 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 305 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 320 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058488 restraints weight = 72475.265| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.26 r_work: 0.2795 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30068 Z= 0.104 Angle : 0.572 15.861 40812 Z= 0.272 Chirality : 0.040 0.147 4700 Planarity : 0.003 0.038 5116 Dihedral : 3.361 13.136 3964 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.05 % Allowed : 11.03 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.14), residues: 3664 helix: 1.42 (0.12), residues: 1896 sheet: 0.88 (0.26), residues: 444 loop : 0.82 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.015 0.001 TYR F 266 PHE 0.048 0.001 PHE A 159 TRP 0.009 0.001 TRP D 275 HIS 0.002 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00234 (30068) covalent geometry : angle 0.57192 (40812) hydrogen bonds : bond 0.03421 ( 1476) hydrogen bonds : angle 3.97501 ( 4074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9442 (mmm) cc_final: 0.8849 (ptm) REVERT: A 154 MET cc_start: 0.9119 (tpt) cc_final: 0.8755 (tpp) REVERT: A 252 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8144 (t80) REVERT: A 372 ASN cc_start: 0.6723 (t0) cc_final: 0.6001 (t0) REVERT: B 154 MET cc_start: 0.8614 (tpp) cc_final: 0.8156 (tpp) REVERT: B 198 TYR cc_start: 0.8963 (t80) cc_final: 0.8559 (t80) REVERT: B 252 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 806 ASN cc_start: 0.8652 (t0) cc_final: 0.8374 (t0) REVERT: C 30 MET cc_start: 0.9433 (mmm) cc_final: 0.8941 (ptt) REVERT: C 154 MET cc_start: 0.8850 (tpp) cc_final: 0.8306 (tpp) REVERT: C 198 TYR cc_start: 0.8899 (t80) cc_final: 0.8548 (t80) REVERT: C 252 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8169 (t80) REVERT: C 806 ASN cc_start: 0.8649 (t0) cc_final: 0.8359 (t0) REVERT: D 154 MET cc_start: 0.8776 (tpp) cc_final: 0.8390 (tpp) REVERT: D 198 TYR cc_start: 0.8781 (t80) cc_final: 0.8386 (t80) REVERT: D 252 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8176 (t80) REVERT: D 372 ASN cc_start: 0.6706 (t0) cc_final: 0.5986 (t0) REVERT: E 260 ARG cc_start: 0.5261 (mtt180) cc_final: 0.3900 (mmt180) REVERT: E 266 TYR cc_start: 0.8355 (m-80) cc_final: 0.7882 (m-80) REVERT: G 266 TYR cc_start: 0.8204 (m-10) cc_final: 0.7975 (m-80) outliers start: 34 outliers final: 15 residues processed: 246 average time/residue: 0.5670 time to fit residues: 170.9177 Evaluate side-chains 242 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 341 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 361 optimal weight: 0.2980 chunk 308 optimal weight: 0.2980 chunk 232 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.088239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059140 restraints weight = 72938.255| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.28 r_work: 0.2792 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30068 Z= 0.101 Angle : 0.560 11.281 40812 Z= 0.269 Chirality : 0.040 0.174 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.323 12.751 3964 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.68 % Allowed : 11.28 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.14), residues: 3664 helix: 1.34 (0.12), residues: 1924 sheet: 0.89 (0.26), residues: 444 loop : 0.87 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 329 TYR 0.016 0.001 TYR A 198 PHE 0.034 0.001 PHE C 144 TRP 0.008 0.001 TRP B 275 HIS 0.002 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00224 (30068) covalent geometry : angle 0.56024 (40812) hydrogen bonds : bond 0.03303 ( 1476) hydrogen bonds : angle 3.96165 ( 4074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9534.67 seconds wall clock time: 163 minutes 28.76 seconds (9808.76 seconds total)